I don't see why not. I know how I'd do it if I was on a Kindle at least... that is what I have experience with.
Someone, I think brianinmaine, posted an extension for KUAL (Kindle Unified Application Launcher). It ran a script which he found somewhere else, which apparently can upload files to a Dropbox account on-demand. You could probably do something similar on the Pocketbook.
Does Pocketbook have a builtin Dropbox client? If so, symlink the annotations folder to the Dropbox sync folder.
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